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haplotype analysis

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https://www.readbyqxmd.com/read/28635424/genome-wide-linkage-and-haplotype-sharing-analysis-implicates-the-mcdr3-locus-as-a-candidate-region-for-a-developmental-macular-disorder-in-association-with-digit-abnormalities
#1
Valentina Cipriani, Ambreen Kalhoro, Gavin Arno, Raquel S Silva, Nikolas Pontikos, Virginie Puech, Michelle E McClements, David M Hunt, Veronica van Heyningen, Michel Michaelides, Andrew R Webster, Anthony T Moore, Bernard Puech
BACKGROUND: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second locus on 5p15-5p13 (MCDR3) has been implicated in a similar phenotype, but the disease-causing mechanism still remains unknown. METHODS: Two families affected by a dominant developmental macular disorder that closely resembles NCMD in association with digit abnormalities were included in the study...
March 2, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28635360/the-association-between-apolipoprotein-a1-c3-a5-gene-cluster-promoter-polymorphisms-and-risk-of-ischemic-stroke-in-the-northern-chinese-han-population
#2
Yanzhe Wang, Fang Liu, Lei Li, Shumin Deng, Zhiyi He
Objective Given its effects on lipid metabolism, the apolipoprotein A1-C3-A5 ( APOA1-C3-A5) gene cluster is thought to play an important role in ischemic stroke pathogenesis. Here, we evaluated whether the APOA1-C3-A5 cluster is associated with ischemic stroke in the northern Chinese Han population. Methods This case-control study analyzed 812 patients with ischemic stroke and 844 healthy controls with regard to four APOA1-C3-A5 cluster promoter single nucleotide polymorphisms (SNPs), rs670, rs2854116, rs2854117, and rs662799, using the SNaPshot Multiplex sequencing assay...
January 1, 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28633917/polymorphic-variants-of-caspase-genes-8-3-in-the-risk-prediction-of-coronary-artery-disease
#3
Kishore Kumar Gundapaneni, Nivas Shyamala, Rajesh Kumar Galimudi, Keerthi Kupsal, Srilatha Reddy Gantala, Chiranjeevi Padala, Padma Gunda, Mohini Aiyengar Tupurani, Kaushik Puranam, Sanjib Kumar Sahu, Surekha Rani Hanumanth
Apoptosis has been involved in a number of pathological conditions including coronary artery disease (CAD). Caspases (CASP) are important regulators and executioners in both extrinsic and intrinsic apoptotic pathways and play a crucial role in the development and progression of CAD. The aim of the present study is to examine the role of Caspase 8 and 3 polymorphisms in the pathogenesis of CAD. 300 CAD patients and 300 healthy controls were genotyped for polymorphisms in CASP8 (-652 6N del/ins, IVS12-19G>A), CASP3 (rs4647601;G>T) by PCR-RFLP...
June 17, 2017: Gene
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#4
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28633351/data-compression-can-discriminate-broilers-by-selection-line-detect-haplotypes-and-estimate-genetic-potential-for-complex-phenotypes
#5
N J Hudson, R J Hawken, R Okimoto, R L Sapp, A Reverter
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers...
June 15, 2017: Poultry Science
https://www.readbyqxmd.com/read/28633069/mitogenomic-diversity-in-russians-and-poles
#6
Boris Malyarchuk, Andrey Litvinov, Miroslava Derenko, Katarzyna Skonieczna, Tomasz Grzybowski, Aleksandra Grosheva, Yuri Shneider, Sergei Rychkov, Olga Zhukova
Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered...
June 15, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28632759/analysis-of-intra-host-genetic-diversity-of-prunus-necrotic-ringspot-virus-pnrsv-using-amplicon-next-generation-sequencing
#7
Wycliff M Kinoti, Fiona E Constable, Narelle Nancarrow, Kim M Plummer, Brendan Rodoni
PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28632076/association-of-oprd1-gene-variants-with-opioid-dependence-in-addicted-male-individuals-undergoing-methadone-treatment-in-the-north-of-iran
#8
Alireza Sharafshah, Hedyeh Fazel, Ali Albonaim, Vahid Omarmeli, Sajjad Rezaei, Ebrahim Mirzajani, Farzam Ajamian, Parvaneh Keshavarz
Genetic association of rs678849 along with neuroimaging and biomarker phenotypes, parallel with the known involvements of the OPRD1 in drug abuse, provided additional support for targeting these receptors as potential therapeutic targets in both neurodegenerative diseases and neuropsychiactric disorders such as Alzheimer's disease. Samples were selected among 202 opium-addicted participants undergoing methadone treatment and 202 healthy controls. Genomic DNA of all subjects was extracted from whole blood samples through a Salting Out procedure...
March 1, 2017: Journal of Psychoactive Drugs
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#9
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28628399/polymorphisms-in-lep-and-lepr-genes-in-infants-correlation-with-serum-leptin-values-in-the-first-6-months-of-life
#10
Francesco Savino, Allegra Sardo, Paola Montanari, Ilaria Galliano, Liliana Di Stasio, Massimiliano Bergallo, Leandra Silvestro
OBJECTIVE: Because several studies indicate that polymorphisms in leptin (Lep) and leptin receptor (Lepr) genes play a central role in determining obesity, we analyzed 2 single nucleotide polymorphisms (SNPs) in the Lep gene (Lep G2548A and A19G) and one in the Lepr gene (Lepr A668G) to verify the effect of the 3 SNPs on leptin concentrations in infancy. METHODS: We enrolled 80 healthy Caucasian infants under 6 months of age, who were genotyped for the 3 SNPs with amplification refractory mutation system-mismatch amplification mutation assay (ARMS-MAMA) real-time polymerase chain reaction (PCR)...
June 19, 2017: Journal of the American College of Nutrition
https://www.readbyqxmd.com/read/28628103/a-common-haplotype-lowers-pu-1-expression-in-myeloid-cells-and-delays-onset-of-alzheimer-s-disease
#11
Kuan-Lin Huang, Edoardo Marcora, Anna A Pimenova, Antonio F Di Narzo, Manav Kapoor, Sheng Chih Jin, Oscar Harari, Sarah Bertelsen, Benjamin P Fairfax, Jake Czajkowski, Vincent Chouraki, Benjamin Grenier-Boley, Céline Bellenguez, Yuetiva Deming, Andrew McKenzie, Towfique Raj, Alan E Renton, John Budde, Albert Smith, Annette Fitzpatrick, Joshua C Bis, Anita DeStefano, Hieab H H Adams, M Arfan Ikram, Sven van der Lee, Jorge L Del-Aguila, Maria Victoria Fernandez, Laura Ibañez, Rebecca Sims, Valentina Escott-Price, Richard Mayeux, Jonathan L Haines, Lindsay A Farrer, Margaret A Pericak-Vance, Jean Charles Lambert, Cornelia van Duijn, Lenore Launer, Sudha Seshadri, Julie Williams, Philippe Amouyel, Gerard D Schellenberg, Bin Zhang, Ingrid Borecki, John S K Kauwe, Carlos Cruchaga, Ke Hao, Alison M Goate
A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU...
June 19, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28627236/estrogen-receptor-1-esr1-gene-polymorphisms-and-obesity-phenotypes-in-a-population-of-young-adults
#12
María Correa-Rodríguez, Jacqueline Schmidt-RioValle, Emilio González-Jiménez, Blanca Rueda-Medina
Obesity is considered an increasingly serious health problem determined by multiple genetic and environmental factors. Estrogens have been found to play a major role in body weight and adiposity regulation through estrogen receptor 1 ( ESR1). The aim of this study was to determine whether genotype and haplotype frequencies of ESR1 polymorphisms are associated with body composition measures in a population of 572 young adults. A lack of significant association between genotypes of ESR1 gene polymorphisms and obesity phenotypes was seen after adjustment for confounding factors...
June 1, 2017: Clinical Nursing Research
https://www.readbyqxmd.com/read/28624874/reliable-molecular-differentiation-of-trichuris-ovis-and-trichuris-discolor-from-sheep-ovis-orientalis-aries-and-roe-deer-capreolus-capreolus-and-morphological-characterisation-of-their-females-morphology-does-not-work-sufficiently
#13
Pavel Vejl, Stanislava Nechybová, Pavla Peřinková, Martina Melounová, Vladimíra Sedláková, Jakub Vašek, Daniela Čílová, Kateřina Rylková, Ivana Jankovská, Jaroslav Vadlejch, Iva Langrová
The main aim of the study was to evaluate associations between morphological variability of Trichuris females from sheep and roe deer and their rDNA polymorphism in whipworm populations from the Czech Republic. The results introduced the use of new molecular markers based on the internal transcribed spacer (ITS)1-5.8S RNA-ITS2 region polymorphisms, as useful tools for the unambiguous differentiation of congeners Trichuris ovis and Trichuris discolor. These markers revealed both parasites in roe deer and in sheep; however, T...
June 17, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28624054/diverticulitis-and-crohn-s-disease-have-distinct-but-overlapping-tumor-necrosis-superfamily-15%C3%A2-haplotypes
#14
Tara M Connelly, Christine S Choi, Arthur S Berg, Leonard Harris, Joel Coble, Walter A Koltun
BACKGROUND: Diverticulitis (DD) and Crohn's disease (CD) have overlapping features including bowel structuring, inflammation, and infection. Tumor necrosis superfamily 15 (TNFSF15) is an immunoregulatory, anti-angiogenic gene. CD has been previously associated with a haplotype of five TNFSF15 single-nucleotide polymorphism alleles: rs3810936 (G allele), rs6478108 (A), rs6478109 (G), rs7848647 (G), and rs7869487 (A). We aimed to determine the TNFSF15 risk haplotype for DD versus controls with a subgroup analysis of youthful DD patients (aged ≤55 y) versus older controls (aged ≥55 y)...
June 15, 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/28623548/genetic-dissection-for-zinc-deficiency-tolerance-in-rice-using-bi-parental-mapping-and-association-analysis
#15
Jae-Sung Lee, Andres Godwin C Sajise, Glenn B Gregorio, Tobias Kretzschmar, Abdelbagi M Ismail, Matthias Wissuwa
Zinc deficiency is a widespread soil constraint in rice production. Here, we present QTL/candidate genes associated with Zn deficiency tolerance identified through bi-parental QTL mapping and genome-wide association analysis. Zinc (Zn) deficiency is a widespread soil constraint in rice production. Despite several physiological studies elucidating Zn deficiency tolerance mechanisms, little is known about genetic factors conferring tolerance. To identify QTL associated with root development, biomass accumulation, and grain yield under Zn deficiency, we combined bi-parental QTL mapping in a population of 200 backcross inbred (BC1F6) lines and genome-wide association analysis using 247 k SNP markers across 140 accessions of an indica diversity panel...
June 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28622696/associations-between-polymorphisms-in-the-il-4-gene-and-renal-cell-carcinoma-in-chinese-han-population
#16
Hao Rong, Xue He, Li Wang, Yongjun He, Longli Kang, Tianbo Jin
Renal cell carcinoma (RCC) is considered to be a kind of cytokine reactive tumor. The research has been suggested that the host immune system can regulate the clinical course of RCC. Therefore, cytokine gene polymorphisms in RCC patients were analyzed was necessary. Our study is purpose to analyzing the interleukin-4(IL-4) polymorphisms associated with RCC risk from Han Chinese population. IL-4 genetic polymorphisms were genotyped using MassARRAY technology from a total of 291RCC and 463 controls. Unconditional logistic regression analysis was performed to analyze their relationship with risk of RCC...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28622394/y-chromosomal-analysis-of-greek-cypriots-reveals-a-primarily-common-pre-ottoman-paternal-ancestry-with-turkish-cypriots
#17
Alexandros Heraclides, Evy Bashiardes, Eva Fernández-Domínguez, Stefania Bertoncini, Marios Chimonas, Vasilis Christofi, Jonathan King, Bruce Budowle, Panayiotis Manoli, Marios A Cariolou
Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages...
2017: PloS One
https://www.readbyqxmd.com/read/28620757/a-novel-homozygous-complex-deletion-in-cftr-caused-cystic-fibrosis-in-a-chinese-patient
#18
Keqiang Liu, Yaping Liu, Xue Li, Kai-Feng Xu, Xinlun Tian, Xue Zhang
Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians, but is considered to be a very rare disease in Chinese population. Here, we present an 11-year-old Chinese CF patient with disseminated bronchiectasis and salty sweat, for whom exon sequencing followed by multiplex ligation-dependent probe amplification analysis of the CFTR gene was applied for mutation screening. A homozygous deletion involving exon 20 of CFTR was observed in the patient's genome. Molecular characterization of the breakpoints indicated that both alleles of this locus had an identical novel complex rearrangement (c...
June 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28617813/identification-of-padi2-as-a-novel-angiogenesis-regulating-gene-by-genome-association-studies-in-mice
#19
Mehrdad Khajavi, Yi Zhou, Amy E Birsner, Lauren Bazinet, Amanda Rosa Di Sant, Alex J Schiffer, Michael S Rogers, Subrahmanian Tarakkad Krishnaji, Bella Hu, Vy Nguyen, Leonard Zon, Robert J D'Amato
Recent findings indicate that growth factor-driven angiogenesis is markedly influenced by genetic variation. This variation in angiogenic responsiveness may alter the susceptibility to a number of angiogenesis-dependent diseases. Here, we utilized the genetic diversity available in common inbred mouse strains to identify the loci and candidate genes responsible for differences in angiogenic response. The corneal micropocket neovascularization assay was performed on 42 different inbred mouse strains using basic fibroblast growth factor (bFGF) pellets...
June 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28617311/inducible-nitric-oxide-synthase-polymorphisms-and-nitric-oxide-levels-in-individuals-with-chronic-periodontitis
#20
Raquel M Scarel-Caminaga, Flávia F Cera, Suzane C Pigossi, Livia S Finoti, Yeon J Kim, Aline C Viana, Rodrigo Secolin, Marcelo F Montenegro, José E Tanus-Santos, Silvana R P Orrico, Joni A Cirelli
This study aimed to investigate whether the -1026(A>C)(rs2779249) and +2087(A>G)(2297518) polymorphisms in the NOS2 gene were associated with chronic periodontitis (CP) and with salivary levels of nitrite (NO₂(-)) and/or nitrate + nitrite (NOx). A group of 113 mixed-race patients were subjected to periodontal, genetic, and biochemical evaluations (65 CP/48 periodontally healthy subjects). DNA was extracted from oral epithelial cells and used for genotyping by polymerase chain reaction (real-time). Salivary NOx concentrations were determined using an ozone-based chemiluminescence assay...
June 15, 2017: International Journal of Molecular Sciences
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